Date of Award


Document Type


Degree Name

Master of Science (MS)

Legacy Department

Plant and Environmental Science

Committee Chair/Advisor

Dr. Paula Agudelo

Committee Member

Dr. Christina Wells

Committee Member

Dr. Patrick Gerard


Background: The semi-endoparasitic reniform nematode (Rotylenchulus reniformis) is a major yield-limiting pest of multiple crops in the tropics and sub-tropics, including upland cotton (Gossypium hirsutum). Reniform-resistant cotton varieties are urgently needed, but genes that confer resistance to reniform nematode have not been identified in any species. Parasitism by reniform nematode involves significant developmental changes in plant roots, leading to the formation of multicellular feeding structures called syncytia. Here, we present de novo transcriptomes assembled from syncytial and non-syncytial cotton roots on three sampling dates across a 12-day time course. Results: Total mRNA samples extracted from reniform-infected and uninfected G. hirsutum roots were sequenced on the Illumina HiSeq 2000 platform, generating over 400 million paired-end reads. A de novo root transcriptome for G. hirsutum was assembled with the Trinity pipeline, generating 156,156 unique contigs with an N50 of 712 bp. After removal of contigs from nematodes and other soil organisms, reads from 18 individual RNA samples were mapped back to the cotton reference transcriptome to quantify gene expression at 3, 9 and 12 days after inoculation (DAI). Overall, 432, 266 and 229 genes were significantly up-regulated and 297, 325, and 232 genes were significantly down-regulated in infected vs. uninfected roots at 3, 9, and 12 DAI, respectively (FDR = 0.05). GO-enrichment analyses identified 48 gene ontology terms that were significantly enriched in the set of 1500 genes differentially expressed on at least one sampling date. These included cell periphery, membrane and plasma membrane, catalytic activity, oxidoreductase activity, and response to stimulus and stress. Five genes were significantly up-regulated in syncytial roots across all sampling dates: an ABC transporter, a cytochrome p450, glutathione s-transferase, a homolog of the multi-drug and toxic compound extrusion gene transparent testa 12, and a bel1 transcription factor. Twenty-eight genes were significantly down-regulated across all sampling dates, many of which were involved in cell wall processes and plant defense. Conclusions: Comprehensive gene expression profiles of syncytial development significantly advance our current understanding of plant resistance to reniform nematode. In future work, we will use these expression data to construct gene network models of syncytium formation, with the long-term goal of disrupting the networks that underlie successful nematode infection. Gaining new insights into the mechanisms of plant response to reniform nematode has practical significance for nematode control through the development of resistant crop varieties.



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